9FY3
Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
This is a non-PDB format compatible entry.
Summary for 9FY3
| Entry DOI | 10.2210/pdb9fy3/pdb |
| EMDB information | 50858 |
| Descriptor | Large ribosomal subunit protein bL32, 50S ribosomal protein L3, 50S ribosomal protein L4, ... (54 entities in total) |
| Functional Keywords | arrest peptide, stalled ribosome complex, bacillus subtilis, apcf, ribosome |
| Biological source | Clostridioides difficile 630 More |
| Total number of polymer chains | 53 |
| Total formula weight | 2167436.66 |
| Authors | Gersteuer, F.,Wilson, D.N. (deposition date: 2024-07-02, release date: 2026-01-14, Last modification date: 2026-05-27) |
| Primary citation | Yoshida, M.,Gersteuer, F.,Berendes, O.,Fujiwara, K.,Safdari, H.A.,Paternoga, H.,Takada, H.,Obana, N.,Grubmuller, H.,Bock, L.V.,Wilson, D.N.,Chiba, S. Diverse mechanisms of translation arrest by a Clostridia ribosome stalling peptide CliM. Nat Commun, 17:-, 2026 Cited by PubMed Abstract: Ribosome arrest peptides undergo programmed translational stalling in response to changes in the cellular environment to feedback-regulate gene expression. CliM, an arrest peptide in Clostridia, is encoded upstream of the YidC membrane protein insertase gene, but its function and mechanism remain unclear. Here we show that CliM monitors YidC activity to maintain adequate cellular YidC capacity. Interestingly, Clostridium kluyveri CliM induces elongation arrest at multiple sense codons, whereas Clostridioides difficile CliM causes termination arrest. Cryo-EM-based structural and mutational analyses demonstrate that C. difficile CliM adopts multiple α-helices within the nascent polypeptide exit tunnel, where it forms extensive arrest-essential interactions with the ribosome. The residue immediately N-terminal to the stalling site contributes to arrest by sterically interfering with full accommodation of the release factor or aminoacyl-tRNA in the A-site. Molecular dynamics simulations suggest that membrane insertion of CliM induces sequential unwinding of these α-helical structures and relocation of the penultimate residue, thereby triggering arrest release. These findings provide a unified mechanistic framework that explains the distinct arrest behaviors of CliM homologs. PubMed: 42151144DOI: 10.1038/s41467-026-72673-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.8 Å) |
Structure validation
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